Source code for ccpn.core.lib.SpectrumDataSources.lib.BinaryHeader

"""
This file the BinaryHeader data access class

it serves as int/float/char translator of the actual spectral header data

"""
#=========================================================================================
# Licence, Reference and Credits
#=========================================================================================
__copyright__ = "Copyright (C) CCPN project (http://www.ccpn.ac.uk) 2014 - 2017"
__credits__ = ("Wayne Boucher, Ed Brooksbank, Rasmus H Fogh, Luca Mureddu, Timothy J Ragan & Geerten W Vuister")
__licence__ = ("CCPN licence. See http://www.ccpn.ac.uk/v3-software/downloads/license",
               "or ccpnmodel.ccpncore.memops.Credits.CcpnLicense for licence text")
__reference__ = ("For publications, please use reference from http://www.ccpn.ac.uk/v3-software/downloads/license",
               "or ccpnmodel.ccpncore.memops.Credits.CcpNmrReference")
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# Last code modification
#=========================================================================================
__modifiedBy__ = "$modifiedBy: CCPN $"
__dateModified__ = "$dateModified: 2017-07-07 16:33:14 +0100 (Fri, July 07, 2017) $"
__version__ = "$Revision: 3.0.b5 $"
#=========================================================================================
# Created
#=========================================================================================
__author__ = "$Author: gvuister $"
__date__ = "$Date: 2020-11-20 10:28:48 +0000 (Fri, November 20, 2020) $"
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# Start of code
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from array import array

[docs]class BinaryHeader(object): """A class to convert binary header data into ints, float or char-strings Used for formats like NmrPipe and Felix, that contain mixed binary header data intValues and floatValues defined in words """ def __init__(self, headerSize, wordSize=4): "Define the object's header size and word size (4 or 8 bytes)" self.headerSize = headerSize self.wordSize = wordSize self.bytes = None self.swappedBytes = False self.intValues = None self.floatValues = None
[docs] def read(self, fp, doSeek=True): """Read and initialise the header from binary file pointed to by fp; return self :param doSeek: seek to start of file if True """ if doSeek: fp.seek(0,0) # rewind the file as header should be at the start # bytes = array('B') # bytes.fromfile(fp, self.headerSize * self.wordSize) bytes = fp.read(self.headerSize * self.wordSize) if len(bytes) < self.headerSize*self.wordSize: raise RuntimeError('%s appears truncated' % self) self.fromBytes(bytes) return self
[docs] def fromBytes(self, bytes): "Intialise the header from bytes; return self" typeCode = 'B' self.bytes = array(typeCode) self.bytes.frombytes(bytes) typeCode = 'i' if self.wordSize == 4 else 'l' self.intValues = array(typeCode) self.intValues.frombytes(self.bytes) typeCode = 'f' if self.wordSize == 4 else 'd' self.floatValues = array(typeCode) self.floatValues.frombytes(self.bytes) return self
@property def bytesAsHexTuple(self): "Return all bytes as a tuple of hexadecimal strings" return tuple(["%02X" % byte for byte in self.bytes])
[docs] def swapBytes(self): "Swap the bytes of intValues and floatValues" self.intValues.byteswap() self.floatValues.byteswap() self.swappedBytes = not self.swappedBytes
[docs] def bytesToString(self, start, stop, strip=False): """Return bytes within range(start,stop) (eg. (10,14) converts bytes 10,11,12,13 to chr and returns it as a string optionally strip string of '\00' """ chars = [chr(self.bytes[i]) for i in range(start,stop)] result = ''.join(chars) if strip: result = result.strip('\x00') return result
[docs] def wordsToString(self, start, stop): """Return words within range(start,stop) (eg. (10,14) converts words 10,11,12,13 to chr and returns it as a string """ result = ''.join([chr(self.intValues[i]) for i in range(start,stop)]) return result